Category Archives: What’s New

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You’ve seen it before on shopping web site: you load a page displaying an item you want and see a list of other items that people bought with the one you’re viewing.

PubMed is free, but finding the important articles on a topic can cost a lot of time. To help you keep on top of the literature – with a little help from your fellow PubMed users – we are introducing a new type of link called “Articles frequently viewed together”. For some PubMed abstracts, you may see this link in the “Related Information” section in the right column.

Figure 1. The PubMed Also-Viewed feature.

Not all abstracts will have this link; currently, only 1.3 million out of the 24 million records in PubMed do. The calculation is based on anonymous click data for the last year, so older articles will be especially underrepresented. To find all articles with these relationships, search PubMed with the query “pubmed_pubmed_alsoviewed[filter]”. Add additional terms to narrow the focus to your area of interest.

Please give it a try and let us know what you think by adding comments to this blog post.

BLAST (Basic Local Alignment Search Tool) is a popular tool for finding sequences in a given database that are similar to a query sequence. Traditionally, BLAST displays these results as a sorted list of matches between the query and each database sequence. While this display is useful for examining how each subject sequence matches the query, it treats all subject sequences the same, regardless of the quality of the sequence data or its annotation, and also does not allow easy comparisons between different subject sequences. For example, the subject sequences may fall into multiple groups of similar sequences, or all of the subject sequences may be more similar to each other than to the query. A common way to obtain this information is to construct a multiple sequence alignment of the query and some or all of the subject sequences, but to this point, BLAST has not provided such alignments directly.

Enter SmartBLAST! SmartBLAST is a new and experimental NCBI tool that makes it easier to answer common sequence analysis tasks, such as finding a candidate protein name for a sequence, locating regions of high sequence conservation, or identifying regions covered by database sequences but missing from the query. To do this, SmartBLAST performs the following tasks in much less time than it takes to run a typical BLASTp search: Continue reading →

Featured

PubMed Labs is all about you. It’s a new NCBI initiative for creating innovative and relevant products by involving you, our user community, from the beginning.

PubMed Labs is about experimentation. It’s a place where you’ll find early versions of new tools, experimental content, and proposed features, as well as an opportunity to suggest ideas to us.

PubMed Labs is about learning. It’s a place where the focus is on figuring out what works, where failure is OK because it’s a learning experience, and where any idea is welcome that can improve our services for our users.

PubMed Labs is about conversation. It’s a place where we can share future plans with you, and you can tell us how we’re doing. It’s a place where we all can come together to create resources that will benefit the broader scientific community.

Join the conversation!

We’re introducing a new category on this blog called “PubMed Labs” that will facilitate this conversation. You can follow these posts by RSS. When we have a new feature for you to try out, we’ll post here with a description of it that will contain the following:

The user need the feature is intended to serve

How you can activate it

What you can expect from it

Our plans for it

Then you can try it out and let us know how it went by commenting on the posts. Like it, hate it, we want to know! Or you can propose some additional functions or ideas.

Our first new features are SmartBLAST, an enhancement to protein BLAST, and an “also-viewed” link in PubMed. Each of these is described in accompanying blog posts:

From January 5th-7th, 2015, NCBI, in conjunction with the NIH Office of Data Science, held a genomics hackathon, where genomics professionals gathered to write useful, efficient pipelines for people new to genomics.

After we announced the hackathon, over 130 qualified applicants expressed interest in attending. Four team leads chose 23 attendees from this pool, then assigned initial predefined roles and provided biological guidance for a product in one of four subject areas: DNA-Seq, RNA-Seq, Epigenomics and Metagenomics. Continue reading →

Antibiotic-resistant bacterial infections account for the deaths of tens of thousands of Americans every year. Over the past twenty years, these difficult to treat infections have become more common. Since traditional antibiotics are ineffective in these cases, biomedical researchers are looking for alternatives. NCBI’s RefSeq project has created a new indexed field, “Protein has antimicrobial activity [prop]“, to assist in this search by retrieving useful sequence annotation showing naturally occurring antimicrobial peptides, or AMPs.

Antimicrobial peptides are naturally occurring peptides from a diverse array of species that are a part of an organism’s innate immune system. The RefSeq team recently gathered a list of over 130 human genes encoding one or more experimentally proven AMPs. These peptides are typically less than 100 amino acids and can display bactericidal, antiviral, antifungal, and even antitumor activities, with a specific AMP usually having a subset of these activities. AMPs may be a suitable alternative to traditional antibiotics because they work quickly, efficiently, and tend to have broad spectrum activity. Moreover, since they are naturally-occurring, AMPs are less likely than other compounds to be toxic to host cells or to give rise to AMP-resistant bacterial strains. Continue reading →

This post is geared toward fungi researchers as well as RefSeq and BLAST users.

Fungi have unique characteristics that can make it difficult to identify and classify species based on morphology. To address these issues, Conrad Schoch, NCBI’s fungi taxonomist, and Barbara Robbertse, NCBI’s fungi RefSeq curator, in collaboration with outside mycology experts, are curating a set of fungal sequences from internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA genes. This set of standard DNA sequences for fungal taxa not only addresses these difficulties in identifying and classifying fungal species by morphology, but is also essential for analyzing environmental (metagenomics) sequencing studies. The curated ITS sequences, described in a recent article in Database (PMC Free Article), all have associated specimen data and, when possible, are taken from sequences from type materials, ensuring correct species identification and tracking of name changes. This article will show you how to access these ITS sequences and search them using the specialized Targeted Loci BLAST service.

The fungal ITS sequences are a RefSeq Targeted Loci BioProject (PRJNA177353). As you may know, a BioProject is a collection of biological data related to a single initiative; in this case, the goal is to collect and curate fungal sequences from targeted loci – specific molecular markers such as protein coding or ribosomal RNA genes used for phylogenetic analysis.

If you’re reading this, you probably already know that NIH and some other institutions have public access policies that require that peer-reviewed publications resulting from their funding be made available to the public. But did you know that if you complied with your funding agency’s public access policy by depositing your author manuscript in NIH’s PubMed Central (PMC) archive via the NIH Manuscript Submission (NIHMS) system, you can easily obtain statistics on how frequently your paper is being accessed? Continue reading →

Today, the NIH Manuscript Submission (NIHMS) system gets a new interface design, as well as updates that streamline the login and manuscript submission processes and provide relevant help information directly on each screen.

Homepage

Figure 1. The new NIH Manuscript Submission system homepage.

The NIHMS sign-in routes will now be available from the homepage. Select a route based on your funding agency (1) or sign in through NCBI if you are starting a deposit on an author’s behalf (2).

The homepage also includes a graphic overview of the NIHMS process (3). You can hover over each step for more information or click “Learn More” to read the complete overview in the FAQ.

In an earlier blog post, we discussed how sequence updates in GRCh38, the most recent version of the human reference genome, filled in a gap in human chromosome 17 near position 21,300K and expanded the region by 500K (500,000 base pairs). In this post, we will again consider this same region, but with an emphasis now on how GRCh38 also improved the gene annotation.

Figure 1. Annotation of a region of chromosome 17 near the KCNJ12 and KCNJ18 genes. Top panel: Annotation release 105 on GRCh37.p13 represented by a configured graphic display of sequence record NC_000017.10. Bottom panel: Annotation release 106 on assembly GRCh38 represented by a configured graphic display of sequence record NC_000017.11. New gene models are circled.

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About the NCBI

The National Center for Biotechnology Information (NCBI), a division of the U.S. National Library of Medicine, provides access to scientific and biomedical databases, software tools for analyzing molecular data, and performs research in computational biology.